Spectral edge detection

ABSTRACT

This disclosure relates generally to detecting multiple biomarkers on or within a sample, though more specifically, to detecting individual detection moieties within a plurality of detection moieties.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/503,118, filed Jul. 3, 2019, which is a continuation-in-part of U.S.application Ser. No. 16/264,490, filed Jan. 31, 2019, now U.S. Pat. No.10,345,237, each of which is herein incorporated by reference in itsentirety.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare incorporated herein by reference in their entirety to the sameextent as if each individual publication or patent application wasspecifically and individually indicated to be incorporated by reference.

FIELD

This disclosure relates generally to detecting multiple biomarkers on orwithin a sample, though more specifically, to detecting individualdetection moieties within a plurality of detection moieties.

BACKGROUND

Samples often include materials of interest that are to be imaged foranalysis. These materials of interest may include a plurality ofbiomarkers and/or components for which it may be desirous to detect andimage. Current filters and imaging apparatuses may only permit for alimited number of labels to be used at any one given time. As a result,practitioners, researchers, and those working with suspensions continueto seek systems and methods to more efficiently and accurately imagesamples.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows an example first emission spectrum.

FIG. 1B shows an example second emission spectrum.

FIG. 1C shows an example third emission spectrum.

FIG. 2A shows an example fourth emission spectrum and a backgroundsignal.

FIG. 2B shows a signal obtained during imaging.

FIGS. 3A-3D show the example first and second emission spectra.

FIG. 3E shows the example first and second emission spectra and a thirdemission spectrum.

FIG. 4A shows an example optical path of a fluorescent microscope.

FIG. 4B shows an example optical path of a fluorescent microscope.

FIG. 4C shows an example optical path of a fluorescent microscope.

FIGS. 5A-5D show first, second, third, and fourth raw images,respectively.

FIG. 5E shows a final image based on at least two of the raw images.

FIG. 5F shows a final image based on at least two of the raw images.

FIG. 5G shows a final image based on at least two of the raw images.

DETAILED DESCRIPTION

This disclosure is directed to a system and method for obtainingspectral data of individual detection moieties from a plurality ofdetection moieties, such as those detection moieties having overlappingspectra, based on emission and/or excitation wavelengths of therespective detection moieties used. This disclosure is further directedto a system and method for recording fluorescent images whiledistinguishing between multiple separate fluorescent targets.

In the following description, the term “raw image” is used to describean image (whether or not visually displayed to an operator or end user)including data or at least one signal, having been captured by a sensoror detector, which has not been processed.

In the following description, the term “final image” is used to describean image (whether or not visually displayed to an operator or end user)including data or at least one signal which has been processed. “Finalimage” can also be used to describe an image (whether or not visuallydisplayed to an operator or end user) which is an output image resultingfrom the comparison and/or analysis of two or more raw or other finalimages.

In the following descriptions, the term “light” is used to describevarious uses and aspects of multiplexing and imaging. The term light isnot intended to be limited to describing electromagnetic radiation inthe visible portion of the electromagnetic spectrum, but is alsointended to describe radiation in the ultraviolet and infrared portionsof the electromagnetic spectrum.

In the following descriptions, the term “sample” is used to describe abiological fluid, a biological semi-solid, a biological solid (which mayremain solid, such as tissue, or may be liquefied in any appropriatemanner), a suspension, a portion of the suspension, a component of thesuspension, or the like.

In the following descriptions, the terms “target analyte” or “targetmaterial” are used to describe a biological material of interest.

In the following descriptions, the term “non-target analyte” is used todescribe a biological material which is not a target analyte.

In the following descriptions, the term “biomarker” is used to describea substance that is present on or within the target analyte or targetmaterial (i.e. intracellular or extracellular the target analyte;internalized, such as through phagocytosis, within the target analyte;or the like). Biomarkers include, but are not limited to, peptides,proteins, subunits, domains, motifs, epitopes, isoforms, DNA, RNA, orthe like. The biomarker may be a target molecule for drug delivery.

In the following descriptions, the term “affinity molecule” is used todescribe any molecule that is capable of binding to or interacting withanother molecule. The interaction or binding can be covalent ornon-covalent. The affinity molecule includes, but is not limited to, anantibody, a hapten, a protein, an aptamer, an oligonucleotide, apolynucleotide, or any appropriate molecule for interacting with orbinding to another molecule (e.g., a biomarker; a molecule of a bindingpair or a complementary molecule, including, without limitation, biotinor an avidin; or, the like).

In the following descriptions, the term “detection moiety” is used todescribe a compound or substance which provides a signal for detection,thereby indicating the presence of another compound or substance, ananalyte, or the like within a sample or specimen. The detection moietycan be fluorescent, such as a fluorescent probe, or chromogenic, such asa chromogenic dye. The fluorescent probe can be a reactive dye, anorganic dye, a fluorescent protein, a quantum dot, non-protein organicmolecules, a nanoparticle (e.g., nanodiamond), or the like.

The detection moiety is a compound or substance which provides a signalfor detection, thereby indicating the presence of another compound orsubstance, an analyte, or the like within a sample or specimen. Thedetection moiety can be used as a tracer, as a label for certainstructures, as a label for biomarkers, or the like. The detection moietycan be distributed or can label the appropriate structure or biomarkersin manners including, but not limited to, uptake, selective uptake,diffusion, and attachment to a linking molecule. The detection moietycan be bound to the biomarker by direct labeling or by indirectlabeling.

The chromogenic dye, which can be used with various enzyme labels (e.g.horseradish peroxidase and alkaline phosphate), includes, but is notlimited to, 3,3′-Diaminobenzidine (DAB), 3-Amino-9-Ethylcarbazole (AEC),4-Chloro-1-Naphtol (CN), P-Phenylenediamine Dihydrochloride/pyrocatechol(Hanker-Yates reagent), Fast Red TR, New Fuchsin, Fast Blue BB, or thelike. Fluorescent probes include, but are not limited to 1,5 IAEDANS;1,8-ANS; 4-Methylumbelliferone; 5-carboxy-2,7-dichlorofluorescein;5-Carboxyfluorescein (5-FAM); 5-Carboxynapthofluorescein;5-Carboxytetramethylrhodamine (5-TAMRA); 5-FAM (5-Carboxyfluorescein);5-HAT (Hydroxy Tryptamine); 5-Hydroxy Tryptamine (HAT); 5-ROX(carboxy-X-rhodamine); 5-TAMRA (5-Carboxytetramethylrhodamine);6-Carboxyrhodamine 6G; 6-CR 6G; 6-JOE; 7-Amino-4-methylcoumarin;7-Aminoactinomycin D (7-AAD); 7-Hydroxy-4-methylcoumarin;9-Amino-6-chloro-2-methoxyacridine; AB Q; Acid Fuchsin; ACMA(9-Amino-6-chloro-2-methoxyacridine); Acridine Orange; Acridine Red;Acridine Yellow; Acriflavin; Acriflavin Feulgen SITSA; Aequorin(Photoprotein); AutoFluorescent Protein; Alexa Fluor 350™; Alexa Fluor430™; Alexa Fluor 488™; Alexa Fluor 532™; Alexa Fluor 546™; Alexa Fluor568™; Alexa Fluor 594™; Alexa Fluor 633™; Alexa Fluor 647™; Alexa Fluor660™; Alexa Fluor 680™; Alizarin Complexon; Alizarin Red;Allophycocyanin (APC); AMC; AMCA-S; AMCA (Aminomethylcoumarin); AMCA-X;Aminoactinomycin D; Aminocoumarin; Aminomethylcoumarin (AMCA); AnilinBlue; Anthrocyl stearate; APC (Allophycocyanin); APC-Cy7; APTRA-BTC;APTS; Astrazon Brilliant Red 4G; Astrazon Orange R; Astrazon Red 6B;Astrazon Yellow 7 GLL; Atabrine; ATTO-TAG™ CBQCA; ATTO-TAG™ FQ;Auramine; Aurophosphine G; Aurophosphine; BAO9(Bisaminophenyloxadiazole); BCECF (high pH); BCECF (low pH); BerberineSulphate; Beta Lactamase; BFP blue shifted GFP (Y66H; Blue FluorescentProtein); BFP/GFP FRET; Bimane; Bisbenzamide; Bisbenzimide (Hoechst);bis-BTC; Blancophor FFG; Blancophor SV; BOBO™-1; BOBO™-3; Bodipy492/515; Bodipy 493/503; Bodipy 500/510; Bodipy 505/515; Bodipy 530/550;Bodipy 542/563; Bodipy 558/568; Bodipy 564/570; Bodipy 576/589; Bodipy581/591; Bodipy 630/650-X; Bodipy 650/665-X; Bodipy 665/676; Bodipy Fl;Bodipy FL ATP; Bodipy Fl-Ceramide; Bodipy R6G SE; Bodipy TMR; BodipyTMR-X conjugate; Bodipy TMR-X, SE; Bodipy TR; Bodipy TR ATP; Bodipy TR-XSE; BO-PRO™-1; BO-PRO™-3; Brilliant Sulphoflavin FF; Brilliant Violet421; Brilliant Violet 510; Brilliant Violet 605; Brilliant Violet 650;Brilliant Violet 711; Brilliant Violet 786; BTC; BTC-5N; Calcein;Calcein Blue; Calcium Crimson™; Calcium Green; Calcium Green-1; CalciumGreen-2; Calcium Green-5N; Calcium Green-C18; Calcium Orange; CalcofluorWhite; Carboxy-X-hodamine (5-ROX); Cascade Blue™; Cascade Yellow;Catecholamine; CCF2 (GeneBlazer); CFDA; CFP (Cyan Fluorescent Protein);CF405S; CF488A; CF 543; CF 568; CF 647; CF 750; CF 780; FP/YFP FRET;Chlorophyll; Chromomycin A; Chromomycin A; CL-NERF; CMFDA;Coelenterazine; Coelenterazine cp; Coelenterazine f; Coelenterazine fcp;Coelenterazine h; Coelenterazine hcp; Coelenterazine ip; Coelenterazinen; Coelenterazine O; Coumarin Phalloidin; C-phycocyanine; CPMMethylcoumarin; CTC; CTC Formazan; Cy2™; Cy3.18; Cy3.5™; Cy3™; Cy5.18;Cy5.5™; Cy5™; Cy7™; Cyan GFP; cyclic AMP Fluorosensor (FiCRhR); CyQuantCell Proliferation Assay; Dabcyl; Dansyl; Dansyl Amine; DansylCadaverine; Dansyl Chloride; Dansyl DHPE; DAPI; Dapoxyl; Dapoxyl 2;Dapoxyl 3; DCFDA; DCFH (Dichlorodihydrofluorescein Diacetate); DDAO; DHR(Dihydorhodamine 123); Di-4-ANEPPS; Di-8-ANEPPS; DiA (4-Di-16-ASP);Dichlorodihydrofluorescein Diacetate (DCFH); DiD-Lipophilic Tracer; DiD(DiIC18(5)); DIDS; Dihydorhodamine 123 (DHR); DiI (DiIC18(3));Dinitrophenol; DiO (DiOC18(3)); DiR; DiR (DiIC18(7)); DM-NERF (high pH);DNP; Dopamine; DsRed; DTAF; DY-630-NHS; DY-635-NHS; EBFP (Enhanced BlueFluorescent Protein); ECFP (Enhanced Cyan Fluorescent Protein); EGFP(Enhanced Green Fluorescent Protein); ELF 97; Eosin; ER-Tracker™ Green;ER-Tracker™ Red; ER-Tracker™ Blue-White DPX; Erythrosin; Erythrosin ITC;Ethidium Bromide; Ethidium homodimer-1 (EthD-1); Euchrysin; EukoLight;Europium (III) chloride; EYFP (Enhanced Yellow Fluorescent Protein);Fast Blue; FDA; FIF (Formaldehyde Induced Fluorescence); FITC; FITCAntibody; Flazo Orange; Fluo-3; Fluo-4; Fluorescein (FITC); FluoresceinDiacetate; Fluoro-Emerald; Fluoro-Gold (Hydroxystilbamidine);Fluor-Ruby; FluorX; FM 1-43™; FM 4-46; Fura Red™ (high pH); FuraRed™/Fluo-3; Fura-2, high calcium; Fura-2, low calcium; Fura-2/BCECF;Genacryl Brilliant Red B; Genacryl Brilliant Yellow 10GF; Genacryl Pink3G; Genacryl Yellow SGF; GeneBlazer (CCF2); GFP (S65T); GFP red shifted(rsGFP); GFP wild type, non-UV excitation (wtGFP); GFP wild type, UVexcitation (wtGFP); GFPuv; Gloxalic Acid; Granular Blue;Haematoporphyrin; Hoechst 33258; Hoechst 33342; Hoechst 34580; HPTS;Hydroxycoumarin; Hydroxystilbamidine (FluoroGold); Hydroxytryptamine;Indo-1, high calcium; Indo-1, low calcium; Indodicarbocyanine (DiD);Indotricarbocyanine (DiR); Intrawhite Cf JC-1; JO-JO-1; JO-PRO-1;LaserPro; Laurodan; LDS 751; Leucophor PAF; Leucophor SF; Leucophor WS;Lissamine Rhodamine; Lissamine Rhodamine B; Calcein/Ethidium homodimer;LOLO-1; LO-PRO-1; Lucifer Yellow; Lyso Tracker Blue; Lyso TrackerBlue-White; Lyso Tracker Green; Lyso Tracker Red; Lyso Tracker Yellow;LysoSensor Blue; LysoSensor Green; LysoSensor Yellow/Blue; Mag Green;Magdala Red (Phloxin B); Mag-Fura Red; Mag-Fura-2; Mag-Fura-5;Mag-Indo-1; Magnesium Green; Magnesium Orange; Malachite Green; MarinaBlue; Maxilon Brilliant Flavin 10 GFF; Maxilon Brilliant Flavin 8 GFF;Merocyanin; Methoxycoumarin; Mitotracker Green; Mitotracker Orange;Mitotracker Red; Mitramycin; Monobromobimane; Monobromobimane(mBBr-GSH); Monochlorobimane; MPS (Methyl Green Pyronine Stilbene);mStrawberry; NBD; NBD Amine; Nile Red; Nitrobenzoxadidole;Noradrenaline; Nuclear Fast Red; Nuclear Yellow; Nylosan Brilliant lavinEBG; Oregon Green™; Oregon Green™ 488; Oregon Green™ 500; Oregon Green™514; Pacific Blue; Pararosaniline (Feulgen); PBFI; PE-Cy5; PE-Cy7;PerCP; PerCP-Cy5.5; PE-TexasRed (Red 613); Phloxin B (Magdala Red);Phorwite AR; Phorwite BKL; Phorwite Rev; Phorwite RPA; Phosphine 3R;PhotoResist; Phycoerythrin B; Phycoerythrin R; PKH26 (Sigma); PKH67;PMIA; Pontochrome Blue Black; POPO-1; POPO-3; PO-PRO-1; PO-PRO-3;Primuline; Procion Yellow; Propidium lodid (PI); Pyrene; Pyronine;Pyronine B; Pyrozal Brilliant Flavin 7GF; QD400; QD425; QD450; QD500;QD520; QD525; QD530; QD535; QD540; QD545; QD560; QD565; QD570; QD580;QD585; QD590; QD600; QD605; QD610; QD620; QD625; QD630; QD650; QD655;QD705; QD800; QD1000; QSY 7; Quinacrine Mustard; Red 613 (PE-TexasRed);Resorufin; RFP; RH 414; Rhod-2; Rhodamine; Rhodamine 110; Rhodamine 123;Rhodamine 5 GLD; Rhodamine 6G; Rhodamine B; Rhodamine B 200; Rhodamine Bextra; Rhodamine BB; Rhodamine BG; Rhodamine Green; RhodaminePhallicidine;

Rhodamine Phalloidine; Rhodamine Red; Rhodamine WT; Rose Bengal;R-phycocyanine; R-phycoerythrin; rsGFP (red shifted GFP (S65T)); S65A;S65C; S65L; S65T; Sapphire GFP; SBFI; Serotonin; Sevron Brilliant Red2B; Sevron Brilliant Red 4G; Sevron Brilliant Red B; Sevron Orange;Sevron Yellow L; sgGFP™ (super glow GFP; SITS (Primuline); SITS(Stilbene Isothiosulphonic Acid); SNAFL calcein; SNAFL-1; SNAFL-2; SNARFcalcein; SNARF1; Sodium Green; SpectrumAqua; SpectrumGreen;SpectrumOrange; Spectrum Red; SPQ(6-methoxy-N-(3-sulfopropyl)quinolinium); Stilbene; Sulphorhodamine Bcan C; Sulphorhodamine G Extra; SYTO 11; SYTO 12; SYTO 13; SYTO 14; SYTO15; SYTO 16; SYTO 17; SYTO 18; SYTO 20; SYTO 21; SYTO 22; SYTO 23; SYTO24; SYTO 25; SYTO 40; SYTO 41; SYTO 42; SYTO 43; SYTO 44; SYTO 45; SYTO59; SYTO 60; SYTO 61; SYTO 62; SYTO 63; SYTO 64; SYTO 80; SYTO 81; SYTO82; SYTO 83; SYTO 84; SYTO 85; SYTOX Blue; SYTOX Green; SYTOX Orange;SYTOX Red; Tetracycline; Tetramethylrhodamine (TRITC); Texas Red™; TexasRed-X™ conjugate; Thiadicarbocyanine (DiSC3); Thiazine Red R; ThiazoleOrange; Thioflavin 5; Thioflavin S; Thioflavin TCN; Thiolyte; ThiozoleOrange; Tinopol CBS (Calcofluor White); TMR; TO-PRO-1; TO-PRO-3;TO-PRO-5; TOTO-1; TOTO-3; TriColor (PE-Cy5);TetramethylRodaminelsoThioCyanate; True Blue; TruRed; Tubulin Tracker™Green; Ultralite; Uranine B; Uvitex SFC; wt GFP (wild type GFP); WW 781;X-Rhodamine; XRITC; Xylene Orange; Y66F; Y66H; Y66W; Yellow GFP (Yellowshifted); Green Fluorescent Protein; YFP (Yellow Fluorescent Protein);YO-PRO-1; YO-PRO-3; YOYO-1; YOYO-3; and, combinations and derivativesthereof. In one embodiment, the detection moiety, such as organicfluorophore, can have a molecule weight of at least 100 Daltons,including, without limitation, at least 1 kD, at least 10 kD, at least25 kD, at least 50 kD, at least 75 kD, at least 100 kD, at least 150 kD,at least 200 kD, at least 250 kD, at least 300 kD, at least 340 kD, atleast 350 kD, at least 500 kD, and at least 750 kD.

In the following descriptions, the terms “stain” or “label,” which areused interchangeably, are used to describe an affinity molecule bound toor interacted with a detection moiety. The binding or interaction can bedirect or indirect. Direct binding or interaction includes covalent ornon-covalent interactions between the biomarker and the detectionmoiety. Indirect binding or interaction includes the use of at leastfirst and second complementary molecules which form binding pairs. Thefirst and second complementary molecules are, in combination, bindingpairs which can bind or interact in at least one of the followingmanners: hydrophobic interactions, ionic interactions, hydrogen bondinginteractions, non-covalent interactions, covalent interactions, affinityinteractions, or the like. The binding pairs include, but are notlimited to, immune-type binding-pairs, such as, antigen-antibody,antigen-antibody fragment, hapten-anti-hapten, or primaryantibody-secondary antibody; nonimmune-type binding-pairs, such asbiotin-avidin, biotin-streptavidin, folic acid-folate binding protein,hormone-hormone receptor, lectin-specific carbohydrate, enzyme-enzyme,enzyme-substrate, enzyme-substrate analog, enzyme-pseudo-substrate(substrate analogs that cannot be catalyzed by the enzymatic activity),enzyme-cofactor, enzyme-modulator, enzyme-inhibitor, or vitaminB12-intrinsic factor. Other suitable examples of binding pairs includecomplementary nucleic acid fragments (including complementarynucleotides, oligonucleotides, or polynucleotides); Protein A-antibody;Protein G-antibody; nucleic acid-nucleic acid binding protein; polymericlinkers (e.g., polyethylene glycol); or polynucleotide-polynucleotidebinding protein. The binding pairs can be included within or used asamplification techniques. Amplification techniques are also implementedto increase the number of detection moieties bound to or interacted withthe biomarker to increase a signal. In one embodiment, when bindingpairs are used, the stain can be pre-conjugated, such that, during alabeling, staining, or adding step, the affinity molecule is alreadybound to or interacted with a detection moiety when added to the sample.In one embodiment, when binding pairs are used, the stain can beconjugated in the sample, such that the labeling, staining, or addingstep includes at least two sub-steps including introducing (in anydesired or appropriate order) an affinity molecule-first bindingmolecule conjugate and a second binding pair molecule-detection moietyconjugate, wherein the first and second binding pair molecules arecomplementary and bind to or interact with each other.

Furthermore, “a plurality of stains” can be used to describe two or morestains in which the affinity molecules and/or the detection moieties aredifferent. For example, anti-CK-Alexa 647 is different thananti-EpCAM-Alexa 647. As another example, anti-CK-Alexa 647 is differentthan anti-CK-Alexa 488.

In the following descriptions, the term “conjugate” is used to describea first chemical, molecule, moiety, or the like bound to or interactedwith a second chemical, molecule, moiety, or the like. The binding orinteraction is direct or indirect. Direct binding or interactionincludes covalent or non-covalent interactions between the biomarker andthe detection moiety. Indirect binding or interaction includes the useof at least first and second complementary molecules which form bindingpairs. The first and second complementary molecules are, in combination,binding pairs which binds or interacts in at least one of the followingmanners: hydrophobic interactions, ionic interactions, hydrogen bondinginteractions, non-covalent interactions, covalent interactions, affinityinteractions, or the like. The binding pairs include, but are notlimited to, immune-type binding-pairs, such as, antigen-antibody,antigen-antibody fragment, hapten-anti-hapten, or primaryantibody-secondary antibody; nonimmune-type binding-pairs, such asbiotin-avidin, biotin-streptavidin, folic acid-folate binding protein,hormone-hormone receptor, lectin-specific carbohydrate, enzyme-enzyme,enzyme-substrate, enzyme-substrate analog, enzyme-pseudo-substrate(substrate analogs that cannot be catalyzed by the enzymatic activity),enzyme-cofactor, enzyme-modulator, enzyme-inhibitor, or vitaminB12-intrinsic factor. Other suitable examples of binding pairs includecomplementary nucleic acid fragments (including complementarynucleotides, oligonucleotides, or polynucleotides); Protein A-antibody;Protein G-antibody; nucleic acid-nucleic acid binding protein; polymericlinkers (e.g., polyethylene glycol); or polynucleotide-polynucleotidebinding protein.

In the following description, the term “signal” is used to describe anelectric current or electromagnetic field which conveys data from oneplace or source to another place or detector. For example, a signal canbe light emitted by a detection moiety to convey the presence of thedetection moiety on or within a target analyte, such as a cell.

In the following description, the term “multiplex” is used to describeprocess or kit by which a sample is labeled with a plurality of stains.Each of the detection moieties emit different wavelengths. For example,at least two stains can be used to label the sample. Multiplexing caninclude up to 2, 4, 6, 8, 10, 12, 16, 20, 24, 30, 40, 50, 60, 70, 80,90, 100, or more stains.

An example method for labeling a biomarker on a target analyte isdiscussed. In one embodiment, a sample, suspected of including at leastone target analyte is obtained. Suitable devices, systems, and/ormethods of sample collection and/or processing may include thosedescribed in one or more of the following U.S. patents and publishedapplications, each of which is hereby incorporated by reference in itsentirety: U.S. Pat. Nos. 7,074,577; 7,220,593; 7,329,534; 7,358,095;7,629,176; 7,915,029; 7,919,049; 8,012,742; 9,039,999; 9,217,697;9,492,819; 9,513,291; 9,533,303; 9,539,570; 9,541,481; 9,625,360;2014/0161688; 2017/0014819; 2017/0059552; 2017/0074759. Suitabledevices, systems, and/or methods for target analyte retrieval,isolation, or picking may include those described in one or more of thefollowing U.S. patents and published applications, each of which ishereby incorporated by reference in its entirety: U.S. Pat. Nos.9,222,953; 9,440,234; 9,519,002; 9,810,605; 2017/0219463; 2017/0276575.

In one embodiment, the sample can undergo staining after collection ofthe sample. In one embodiment, the sample can undergo staining afterprocessing the sample. In one embodiment, the sample can be multiplexed.At least one stain is added to the sample for labeling, such as by anautostainer or manually by an operator. In one embodiment, the at leastone target analyte is stained. In one embodiment, at least onenon-target analyte or non-target material is stained. In one embodiment,the at least one target analyte and the at least one non-target analyteor materials are stained.

After staining, the sample can be imaged, whereby the stained sample isilluminated with one or more wavelengths of excitation light, such asinfrared, red, blue, green, and/or ultraviolet, from a light source,such as a laser or a light-emitting diode. The imaging can be done witha flow cytometer or a microscope, such as a fluorescent microscope, ascanner, or any other appropriate imaging system or modality. In oneembodiment, imaging can be performed in a system in which a detectionmoiety, when imaged, can provide a signal across a spectrum, including,without limitation, brightfield and/or darkfield illumination,fluorescence, and the like. The images formed can be overlaid when aplurality of detection moieties is used. Emission, reflection,diffraction, scatter, and combinations thereof are used in fordetection/imaging. The images can be analyzed to detect, enumerate,and/or locate the target analyte, such as when it is desirous toretrieve or pick the target analyte. Imaging is performed in a tube, ona microscope slide, or in any appropriate vessel or substrate forimaging.

The methods can be performed by at least one of an imaging microscope, ascanner, a flow cytometer, or a microfluidic device, such as a chip or amicrochannel, or the method can be performed by any combination of theabove. The methods described can be used in a system in which adetection moiety, when imaged, can provide a signal across a spectrum,including, without limitation, brightfield and/or darkfieldillumination, fluorescence, and the like.

Spectral Edge Detection

Spectral edge detection is process by which components of a sample aredistinguished from other components of the sample by determining thecontribution of the component of the sample within one or more signals.For example, the sample component can be a detection moiety, a chemical,a biomolecule, a structure, a compound, a substance, a deposit, thelike, or combinations thereof. In other words, spectral edge detectionis process by components having an emission spectrum can bedistinguished from other components.

In one aspect, spectral edge detection is a process by which individualdetection moieties can be distinguished from a plurality of detectionmoieties (i.e., during multiplexing), such as by distinguishing thedetection moieties orthogonally—in that there is no ambiguity as towhich detection moiety is being detected and/or imaged. A feature of asignal of interest, such as from a detection moiety of interest, can bedistinguished in the presence of a featureless signal (i.e., the signalhas an unknown value and/or structure), such as from background,autofluorescence, or a non-desired detection moiety. In other words,spectral edge detection determines the contribution of a detectionmoiety of interest across a plurality of signals (or images) composed ofcontributions from a plurality of detection moieties having at leastpartially overlapping spectra by eliminating the contributions from thenon-desired detection moieties across the plurality of the signals (orimages) when the intensities (and therefore the respectivecontributions) of the detection moieties are unknown.

Raw images are acquired at a given wavelength, for example, at a givenemission wavelength, of the emission spectra. Each raw image includes atotal signal. Each total signal comprises one or more signals from oneor more detection moieties. Each total signal can further comprise asignal due to background or autoflurescence.

Spectral edge detection can also account for minor changes in signals,for example, when detecting a detection moiety against a referencedetection moiety or when incorporating detection moieties which haveemission shifts based on one or more factors, whether intentional (e.g.,detection moieties which detect sample variables, including, forexample, oxygen concentration, metal ion concentation, environmentalchanges, being endocytossed, eing exocytosed, or the like) or whetherunintentional (e.g., variable pH of the sample or reagents causesdetection moieties to have an emission shift).

Spectral edge detection uses an edge (e.g., a trailing edge or a leadingedge) of an emission or excitation spectrum, such as for a detectionmoiety, to identify a single detection moiety within a plurality ofspectrally-overlapping detection moieties. For example, two raw imagescan be obtained along the same leading or trailing spectral edge of thedetection moiety; two raw images can be obtained along different leadingand trailing spectral edges of the detection moiety; or, one raw imagecan be obtained along the leading or trailing spectral edge of thedetection moiety and one raw image can be obtained at the peak emissionof the detection moiety. Spectral edge detection can also utilize acombination of the implementations discussed above for a singledetection moiety or for a plurality of detection moieties. For example,when using a plurality of detection moieties, a first detection moietycan be detected with signals from a peak and a leading spectral edge; asecond detection can be detected with signals from a leading spectraledge; a third detection can be detected with signals from a leadingspectral edge and a trailing spectra edge. Furthermore, spectral edgedetection can form a curve for a first detection moiety and a line for asecond detection moiety, such that at least a portion of the line fallsunder the curve, with data points of each emission spectrum (forexample, signals at given emission/excitation wavelengths).

FIG. 1A shows an emission spectrum 102 of a first detection moiety. Theemission spectrum 102 includes a leading spectral edge 104 and atrailing spectral edge 106. In other words, the leading spectral edge104 is a portion of the emission spectrum 102 to the left of a peakemission 108; the trailing spectral edge 106 is a portion of theemission spectrum 102 to the right of the peak emission 108. Though theemission spectrum 102 is shown, the spectrum can also be an excitationspectrum.

FIG. 1B shows an emission spectrum 110 of a second detection moiety. Theemission spectrum 110 includes a leading spectral edge 112 and atrailing spectral edge 114. In other words, the leading spectral edge112 is a portion of the emission spectrum 110 to the left of a peakemission 116; the trailing spectral edge 114 is a portion of theemission spectrum 110 to the right of the peak emission 116. Though theemission spectrum 110 is shown, the spectrum can also be an excitationspectrum.

FIG. 1C shows an emission spectrum 120 of a third detection moiety. Theemission spectrum 120 includes a leading spectral edge 122 and atrailing spectral edge 124. In other words, the leading spectral edge122 is a portion of the emission spectrum 120 to the left of a peakemission 126; the trailing spectral edge 124 is a portion of theemission spectrum 120 to the right of the peak emission 126. Though theemission spectrum 120 is shown, the spectrum can also be an excitationspectrum.

In one embodiment, any of the methods or systems can be used to detect astain or detection while removing background or autofluorescence from animage or a signal. For example, two or more raw images of a firstdetection moiety are provided, such that at least one of the images isat a lower end of a spectral edge of the first detection moiety and atleast one the images is at a higher end of the spectral edge of thefirst detection moiety. At least one of the raw images includes a signalcaused by autofluorescence or background. A first final image of thefirst detection moiety is provided, such that the first final imagebased on the raw images from the first detection moiety, and the firstfinal image does not include the signal caused by the autofluorescenceor background. This can be performed for any number of detectionmoieties to remove background or autofluorescence from any images.

In FIGS. 2A and 2B, a fourth detection moiety (as depicted by emissionspectrum 204) is used as an example for the method by which anindividual detetion moiety is distinguished over background orautofluorescnece. It should be noted, however, that the method discussedherein is not so limited and can also be implemented on the first,second, and/or third detection moieties (as depicted by emission spectra102, 110, 120) or any other appropriate detection moiety.

FIG. 2A shows the emission spectrum 204 and a background signal 202. Thebackground signal 202 is expected to be relatively unvarying withrespect to the signal of interest and therefore depicted as a constant(i.e., a straight line) with a known value. Additionally, the relativeintensities between the emission spectrum 204 and the background signal202 are unknown.

For clarification purposes, FIGS. 2B-3E depict images I₁-I₁₈ obtainedfrom of a single wavelength. However, the images I₁-I₁₈ can obtainedacross a given bandwidth (i.e., up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, or morenm), such that the images (as denoted by the dot-dot-dash lines) denotethe average signal across the respective bandwidths. Additionally,though raw images are obtained, the signals (for example, the totalsignals comprising the individual signals) are from pixels in the rawimages corresponding to an identical location of the sample betweenimages. For example, Point A is a given location on or within the samplebeing imaged. A first pixel representing Point A in a first raw imagecomprises a first total signal. A second pixel representing Point A in asecond raw image comprises a second total signal. Using one or more ofthe methods discussed herein, the first and second total signals of thefirst and second pixels of the first and second raw images,respectively, are assessed and/or compared to determine thecontribution(s) of the individual detection moiet(ies).

FIG. 2B shows raw images I₁ and I₂ including first and second signals S₁and S₂, respectively, obtained during imaging. The signals S₁ and S₂denote the total contributions of the fourth detection moiety and thebackground 202. Raw image I₁ includes the first signal S₁ on a lower endof the leading spectral edge; and raw image I₂ is taken at a higher endof the leading spectral edge. To identify the fourth detection moiety(as shown by the emission spectrum 204), the raw images I₁ and I₂, areanalyzed and the relative contribution of the fourth detection moietybetween first and second signals S₁ and S₂ is determined by processing,comparing, and/or analyzing the change in signal with any appropriatemathematical, computational, or algebraic process or transformation,including, without limitation, subtraction, derivatives, or combinationsthereof. A final image can then be provided depicting the fourthdetection moiety based on the processing, comparing, and/or analyzing.

Spectral edge detection can be implemented for each detection moietywithin the plurality of detection moieties, thereby allowing formultiplexing of a sample or fraction thereof with any desired number ofdetection moieties. In one embodiment, at least two detection moietiescan be used for multiplexing. In one embodiment, any appropriate numberof detection moieties can be used, including 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 16, 20, 24, 28, 30, 32, 40, 50, 60, 70, 80, 90, or 100. In oneembodiment, any appropriate number of detection moieties can be used,including up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 20, 24, 28, 30,32, 40, 50, 60, 70, 80, 90, or 100. In one embodiment, any appropriatenumber of detection moieties can be used, including less than 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 16, 20, 24, 28, 30, 32, 40, 50, 60, 70, 80, 90,or 100.

Spectral edge detection can be implemented for detetion moieties havingspectral offsets, where the spectral offsets are spectral differences onthe comparable spectral edge or at the spectral peaks. In oneembodiment, this process can be implemented for detection moietieshaving differences in spectral offsets of less than or equal to 50 nm.In one embodiment, this process can be implemented for detectionmoieties having differences in spectral offsets of less than or equal to10 nm. In one embodiment, this process can be implemented for detectionmoieties having differences in spectral offsets of 1-50 nm. In oneembodiment, this process can be implemented for detection moietieshaving differences in spectra of 10-50 nm. In one embodiment, thisprocess can be implemented for detection moieties having differences inspectral offsets of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 20, 25,30, 40, 50, 60, 70, 75, 80, 90, or 100 nm. In one embodiment, thedifference between successive spectra (such as at the peak) can be thesame (e.g., first and second detection moieties are separated by 10 nmand second and third detection moieties are separated by 10 nm). In oneembodiment, the differences between successive spectra (such as at thepeak) can be different (e.g., first and second detection moieties areseparated by 10 nm and second and third detection moieties are separatedby 25 nm).

In one embodiment, the signal contributions of each detection moiety(for example, by way of the contribution or subtraction coefficients)can be determined with at least two raw images, such as by cancellingout or nullifying the signal contributions provided by thenon-interested detection moiety (i.e., a first detection moiety is thenon-interested detection moiety and a second detection moiety is thedetection moiety of interest; and/or, then the first detection moiety isthe detection moiety of interest and the second detection moiety is thenon-interested detection moiety) or background/autofluorescence. Anynumber of raw images equal to or greater than 2 can be obtained forspectral edge detection, including, without limitation, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, ormore.

For clarity purposes regarding FIGS. 3A-3E, the emission spectrum 102 ofthe first detection moiety is also designated by “A”; the emissionspectrum 110 of the second detection moiety is also designated by “B”;and, the emission spectrum 120 of the third detection moiety is alsodesignated by “C.” The subscripts following A, B, or C in thisdescription designate the image to which the detection moiety ofinterest is contributing intensity. For example, a data point A₃ denotesthe contribution of A (or, the first detection moiety) within raw imageI₃, as shown by the data point A₃ on the emission spectrum 102. So,A₃-A₁₈ denote the contributions of A (or, the first detection moiety) inraw images I₃-I₁₈, respectively; B₃-B₁₈ denote the contributions of B(or, the second detection moiety) in raw images I₃-I₁₈, respectively;and, C₃-C₁₈ denote the contributions of C (or, the third detectionmoiety) in raw images I₃-I₁₈, respectively.

FIG. 3A shows the emission spectra 102, 110 for the first and seconddetection moieties. Raw images I₃, I₄, and I₅ are obtained. Raw image I₃is taken at a lower end of the leading spectral edge 104; raw image I₄is taken at a higher end of the leading spectral edge 104, which alsooverlaps with a lower end of the leading spectral edge 112; and, rawimage I₅ is taken at a higher end of the leading spectral edge 112.Though the emission spectra 102, 110 are shown, the spectra can also beexcitation spectra.

In one embodiment, more than three raw images can be obtained. In oneembodiment, each of the raw images are used to analyze one and only oneof the detection moieties. In one embodiment, one or more of the rawimages are used to analyze at least two of the detection moieties (i.e.,there is an overlap). In one embodiment, none of the raw images betweenthe first and second detection moieties are the same (i.e. all imagesare distinct). In one embodiment, at least one of the raw images of thefirst detection moiety and at least one of the raw images of the seconddetection moiety is the same image.

In one embodiment, a raw image taken at the higher end of the trailingspectral edge can include the higher end of the leading spectral edge,and vice-versa (i.e., a raw image taken at the higher end of the leadingspectral edge can include the higher end of the trailing spectral edge).In one embodiment, a raw image taken at the higher end of the particularspectral edge does not include the higher end of the opposing spectraledge (i.e., raw image at higher trailing spectral edge does not includehigher leading spectral edge; raw image at higher leading spectral edgedoes not include higher trailing spectral edge).

To identify a first detection moiety (as shown by the emission spectrum102) and a second detection moiety (as shown by the emission spectrum110), the raw images I₃, I₄, and I₅ are analyzed and the relativecontributions of the first and second detection moieties are determined.For example, the relative contributions can be determined by anyappropriate mathematical, computational, or algebraic process ortransformation, including, without limitation, subtraction, derivatives,or combinations thereof. A final image of the first detection moiety isthen provided based on the analysis of raw images I₃, I₄, such as therelative contribution of the first detection moiety across the rawimages I₃, I₄. A final image of the second detection moiety is thenprovided based on the analysis of raw images I₄, I₅, such as therelative contribution of the second detection moiety across the rawimages I₄, I₅.

FIG. 3B shows the example first and second emission spectra similar tothat of FIG. 3A, except having obtained raw images I₆, I₇, and I₈. Rawimages I₆ and I₈ are taken at points where the emission intensity of thefirst detection moiety has the same or substantially the same value andthe emission intensity of the second detection moiety is differentbetween the images. Raw image I₇ is take at a point such that the atleast three data points for the second detection moiety form a line.

FIG. 3C shows the example first and second emission spectra similar tothat of FIG. 3A, except having obtained raw images I₉ and I₁₀. Rawimages I₉ and I₁₀ are taken at points where a higher end of a spectraledge of the first detection moiety overlaps with a lower end of adifferent spectral edge of the second detection moiety, and where alower end of the spectral edge of the first detection moiety overlapswith a higher end of the different spectral edge of the second detectionmoiety. As shown in FIG. 3C, the trailing edge of the first detectionmoiety overlaps with the leading edge of the second detection moietysuch that raw image I₉ includes the higher end of the trailing spectraledge of the first detection moiety and the lower end of the leadingspectral edge of the second detection moiety, and raw image I₁₀ includesthe lower end of the trailing spectral edge of the first detectionmoiety and the higher end of the leading spectral edge of the seconddetection moiety. In one embodiment, the leading edge of the firstdetection moiety overlaps with the trailing edge of the second detectionmoiety.

FIG. 3D shows the example first and second emission spectra similar tothat of FIG. 3C, except having obtained raw images I₁₁-I₁₄. Raw imagesI₁₂ and I₁₃ are taken at the peaks of emission spectrum 102 and emissionspectrum 110, respectively. The peak emission of a spectrum can be usedto determine the relative contribution of a detection moiety between rawimages, wherein the other raw image is in a spectral edge (leading ortrailing) of the emission spectrum of the detection moiety for which thepeak emission is acquired.

In one embodiment, two or more raw images of a first emission spectrumare obtained, wherein at least one of the images is at a lower end of aspectral edge of the first emission spectrum and at least one the imagesis at a higher end of the same spectral edge of the first emissionspectrum. Two or more raw images of a second emission spectrum areobtained, wherein at least one of the images is at a lower end of aspectral edge of the second emission spectrum and at least one theimages is at a higher end of the same spectral edge of the secondemission spectrum. A first final image of a first detection moiety (asdepicted by the first emission spectrum) and a second final image of asecond detection moiety (as depicted by the second emission spectrum)are provided, wherein the first and second final images are based on theraw images from the first and second detection moieties. In oneembodiment, at least one of the raw images of the first and secondemission spectra is the same image. For example, the second image of thefirst emission spectrum (at the higher end of the first emissionspectrum's spectral edge) is the same image as the first image of thesecond emission spectrum (at the lower end of the second emissionspectrum's spectral edge).

Though two detection moieties are discussed, this process can be usedfor any number of detection moieties. In other words, two or more rawimages of a n^(th) emission/excitation spectrum are obtained, wherein atleast one of the images is at a lower end of a spectral edge of then^(th) emission/excitation spectrum and at least one the images is at ahigher end of the spectral edge of the n^(th) emission/excitationspectrum, and wherein n is greater than or equal to 1 (i.e., 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 16, 20, 24, 28, 30, 32, 40, 50, 60, 70, 80,90, 100, or more). This process is then repeated for at least one moreemission/excitation spectrum.

In one embodiment, to determine signal contribution by individualdetection moieties having overlapping spectra, at least three datapoints of one detection moiety are to be obtained, such that the threedata points form a curve; and, at least two data points of anotherdetection moiety are to be obtained, such that the two data points forma line. The determination as to which detection moiety requires the datapoints to form the curve or the data points to form the line are basedon the relative spectral edges. In other words, when using the samespectral edge (i.e., leading or trailing) of different emission spectra,the emission spectrum having at least a portion of the same spectraledge fall under the emission spectrum of the other emission spectrumonly requires at least two data points. The at least two data points(i.e., those forming the line) can be used to determine the contributionof the detection moiety whether in the presence or absence of the curveprovided by the other detection moiety; and, additionally, the at leastthree data points (i.e., those forming the curve—whether at least twoare in the same spectral edge or whether one is at the peak intensity)can be used to determine the contribution of the other detection moietywhether in the presence or absence of the line provided by the initialdetection moiety.

In one embodiment, to determine signal contribution by individualdetection moieties having overlapping spectra, at least three datapoints of one detection moiety are acquired, such that the three datapoints form a curve; and, at least three data points of anotherdetection moiety are acquired, such that the three data points form acurve or line. For example, in referring back to FIG. 3D, the datapoints of B₁₂-B₁₄ can be incorporated into the following equation:C _(B) =S _(B13)−½(S _(B12) +S _(B14))where CB is the curvature (e.g., second derivative) of emission B,S_(B12) is the signal intensity of emission B at the wavelength of imageI₁₂, S_(B13) is the signal intensity of emission B at the wavelength ofimage I₁₃, and S_(B14) is the signal intensity of emission B at thewavelength of image I₁₄. The data points of A₁₂-A₁₄ can be incorporatedinto the following equation:C _(A) =S _(A13)−½(S _(A12) +S _(A14))where CA is the curvature (e.g., second derivative) of emission A,S_(A12) is the signal intensity of emission A at the wavelength of imageI₁₂, S_(A13) is the signal intensity of emission A at the wavelength ofimage I₁₃, and S_(A14) is the signal intensity of emission A at thewavelength of image I₁₄. The detection moieties are distinguishable fromeach other because a stronger curvature (i.e., more positive (forexample, +5 is stronger than +2; as another example, +4 is stronger than−1) or more negative (for example, −6 is stronger than −1; as anotherexample, −5 is stronger than +2)) at those emission wavelengthscorresponds to individual detection moieties. In other words, detectionmoieties have stronger curvatures across different emission wavelengths.For example, Alexa 647 has a stronger curvature across 660 nm, 670 nm,and 680 nm than Alexa 594 across the same emission wavelengths. Alexa594 has a stronger curvature across 609 nm, 619 nm, and 632 nm thanAlexa 647 across the same emission wavelengths. Therefore, based on thecurvatures across 660 nm, 670 nm, and 680 nm, Alexa 647 can bedistinguished from Alexa 594; and, based on the curvatures across 609nm, 619 nm, and 632 nm, Alexa 594 can be distinguished from Alexa 647.

FIG. 3E depicts three emission spectra 102, 110, 120 (A, B, C) withinfour images I₁₅-I₁₈. A leading edge of emission B is underneath aleading edge of emission A. Therefore, at least three data points areobtained for emission A (e.g., A₁₅-A₁₇; or, A₁₅, A₁₆, A₁₈), and at leasttwo data points are obtained for emission B (e.g., Bis and B₁₆; or, Bisand B₁₇; or, B₁₆ and B₁₇). Additionally, a leading edge of emission C isunderneath a leading edge of emission B. Therefore, at least three datapoints are obtained for emission B (e.g., Bis, B₁₇, B₁₈; or, B₁₆-B₁₈),and at least two data points are required for emission C (e.g., C₁₆ andC₁₇; or, C₁₇ and C₁₈; or, C₁₆ and C₁₈). The respective data points forthe emissions A-C can be used to determine the respective contributionsof the detection moieties.

In one embodiment, two or more raw images at two distinct emissionwavelengths of a first emission spectrum are obtained, wherein at leastone of the images is in a leading spectral edge or a trailing spectraledge of the first emission spectrum and at least one of the images is inthe trailing spectral edge or the leading spectral edge of the firstemission spectrum. In other words, the two or more raw images are indifferent spectral edges of the same emission spectrum (i.e., at leastone raw image in a leading spectral and at least one raw image in atrailing edge, wherein the leading spectral edges are in an emissionspectrum of one detection moiety). As shown in FIG. 3E, signals ofemission spectra A and B are acquired via raw images on differentspectral edges of their emission spectra (A₁₅ and A₁₇ for emissionspectrum A; and, B₁₅/B₁₆/B₁₇ and B₁₈ for emission spectrum B). Theintensities of the signals on the different spectral edges can be equalor not equal (for example, the intensity can be greater on one spectraledge and less on the other spectral edge).

In one embodiment, two or more raw images of a first emission spectrumare obtained, wherein at least one of the raw images is in a leadingspectral edge or a trailing spectral edge of the first emissionspectrum, at least one of the raw images is in the trailing spectraledge or the leading spectral edge of the first emission spectrum, and atleast one of the raw images is at the peak intensity wavelength. Inother words, two or more raw images are in different spectral edges ofthe same emission spectrum and one raw image is at the peak intensitywavelength. As shown in FIG. 3E, emission spectrum A provides signals ondifferent spectral edges of its emission spectra (A₁₅ and A₁₇ foremission spectrum A) and a signal at the peak intensity wavelength (A₁₆for emission spectrum A).

Though FIG. 3E shows raw images acquired from emission spectrum A in theleading spectral edge, the peak emission, and the trailing spectraledge, this is not intended to be limited to only one emission spectrum.The same types of raw images can be acquired for as many emissionspectra as desired.

In yet another aspect, chemicals, biomolecules, structures, compounds,substances, deposits, or the like can be distinguished, whether with orwithout being labeled or stained with a detection moiety. Thenon-detection moiety component, in a manner similar to the detectionmoieties discussed above, emits wavelengths when stimulated therebyforming an emission spectrum. The emission spectrum can be inherent tothe non-detection moiety component, such that different non-detectionmoiety components have different emission spectra. The non-detectionmoiety components, however, comprise autofluorescent emission spectra.In other words, the non-detection moiety components need not be labeledor stained with detection moieties to provide a signal. Thenon-detection moiety components fluoresce due to natural propertiesinherent in their own composition, structure, or the like. Theautofluorescent emission spectrum is used to distinguish thenon-detection moiety component from detection moieties and othernon-detection moiety components having overlapping emission spectra.

The same techniques, methods, and/or protocols discussed above and belowcan be applied to autofluorescent emission spectra, including thoseautofluorescent emission spectra provided by non-detection moietycomponents. Furthermore, as noted in FIGS. 2A-2B, the techniques,methods, and/or protocols discussed above and below can be applied tosamples comprising detection moieties and non-detection moietycomponents.

Non-detection moiety components include, but are not limited to, nuclei,cytoplasm, cytosol, cell membrane, cell wall, fibers, cartilage, cells,interstitial fluid, proteins, glycoproteins, peptides, carbohydrates,nucleic acids, cytochromes, flavins, collagen, lipids, otherbiomolecules, intra-cellular and extra-cellular deposits, foreignmaterials, the like, and combinations thereof.

In one embodiment, change in signal intensity (i.e., pixel levels) canbe used to identify a detection moiety.

In one embodiment, such as when representative points of the emissionspectrum are obtained, the rate of change or the change in signalintensity can be determined based on the trailing edge of the spectrum.In one embodiment, such as when representative points of the emissionspectrum are obtained, the rate of change or the change in signalintensity can be determined based on the leading edge of the spectrum.

In one embodiment, such as when representative points of the excitationspectrum are obtained, the rate of change or the change in intensity canbe determined based on the trailing edge of the spectrum. In oneembodiment, such as when representative points of the excitationspectrum are obtained, the rate of change or the change in intensity canbe determined based on the leading edge of the spectrum.

In one embodiment, the change in signal intensity can be comparedagainst an expected value. For example, the change in intensity can bethe expected value+/−(plus or minus) up to 0.01%, 0.02%, 0.05%, 0.1%,0.15%, 0.2%, 0.25%, 0.3%, 0.35%, 0.4%, 0.45%, 0.5%, 0.55%, 0.6%, 0.65%,0.7%, 0.75%, 0.8%, 0.85%, 0.9%, 0.95%, 1%, 2%, 5%, 10%, 15%, 20%, 25%,30%, 33%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, or 99%. In one embodiment, the change in signal intensity can becompared against a threshold. In one embodiment, the change in signalintensity can be positive or negative, such that the positive ornegative change identifies the desired detection moiety.

In one embodiment, a threshold can be applied, such as during imageprocessing and analysis, to determine whether the signal is caused bythe desired detection moiety, an undesired detection moiety, noise, orbackground.

In one embodiment, when a change in signal intensity between the firstand second images, such as at a desired or pre-determined wavelength, isequal to or greater than a first threshold value, the pixel or signal is“kept on” for the resulting image for analysis; whereas when a change insignal between the first and second images is less than the firstthreshold value, the pixel or signal is “turned off” for the resultingimage for analysis.

In one embodiment, a first emission derivative of the emission spectrum102 of the first detection moiety can be obtained; and, a secondemission derivative of the emission spectrum 110 of the second detectionmoiety can be obtained. Though a first-order derivative is discussed,any higher-order derivative can be calculated when it is desirous to doso.

In one embodiment, such as when representative points of the emissionspectrum are obtained, the rate of change can be greater than or equalto a threshold value. In one embodiment, such as when representativepoints of the emission spectrum are obtained, the change in intensitycan be positive, positive by at least a threshold amount, and/orpositive by a certain multiple of the first emission. In one embodiment,such as when representative points of the excitation spectrum areobtained, the rate of change can be less than or equal to a thresholdvalue (i.e. more negative—for example −5 is less than −3). In oneembodiment, such as when representative points of the excitationspectrum are obtained, the change in intensity can be negative, negativeby at least a threshold amount, and/or negative by a certain multiple ofthe first excitation.

As an example, Δx (the change in emission wavelength) is 10 nm and Δy(the change in emission intensity) is 50%, the slope is 50%/10 nm, or5%/nm. When comparing the first and second images, an increase ofintensity of at least 5 times between respective pixels can beattributed to the first detection moiety and the pixel is “kept on”;whereas an increase of intensity of less than 5 times between respectivepixels can be attributed to something other than the first detectionmoiety (e.g., background) and the pixel is “turned off.” The example isnot intended to be limited to values and/or percentages. The firstthreshold value can include a range based on the anticipated or expectedchange of emission intensity. For example, the first threshold value canbe the slope+/−(plus or minus) up to 0.01%, 0.02%, 0.05%, 0.1%, 0.15%,0.2%, 0.25%, 0.3%, 0.35%, 0.4%, 0.45%, 0.5%, 0.55%, 0.6%, 0.65%, 0.7%,0.75%, 0.8%, 0.85%, 0.9%, 0.95%, 1%, 2%, 5%, 10%, 15%, 20%, 25%, 30%,33%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or99%.

The slope satisfies the condition given by:

${slope} = {\frac{\begin{matrix}{{{intensity}\mspace{14mu}{of}\mspace{14mu}{the}\mspace{14mu}{second}\mspace{14mu}{emission}} -} \\{{intensity}\mspace{14mu}{of}\mspace{14mu}{the}\mspace{14mu}{first}\mspace{14mu}{emission}}\end{matrix}}{\begin{matrix}{{{wavelength}\mspace{14mu}{of}\mspace{14mu}{the}\mspace{14mu}{second}\mspace{14mu}{emission}} -} \\{{wavelength}\mspace{14mu}{of}\mspace{14mu}{the}\mspace{14mu}{first}\mspace{14mu}{emission}}\end{matrix}}.}$

In one embodiment, when exciting the first detection moiety (and therebyobtaining a first image), a wavelength of a first excitation light canbe selected to not excite the second detection moiety. Then, awavelength of a second excitation light can also be selected to excitethe first detection moiety (thereby providing a second image) and to notexcite the second detection moiety. The first and second images can beprocessed and compared to obtain the change of emission intensity (inother words, the slope, or y/x) based on the emissions of the firstdetection moiety due to the change in excitation wavelengths.

In one embodiment, at least one of the excitation lights can stimulateone or more detection moieties. However, the resulting slopes, asdiscussed below, can be used to remove the signal of one or morenon-desired detection moieties.

In one embodiment, two or more images, resulting from the two or moreexcitation wavelengths can be compared and processed to calculate thedesired slope. The resulting slope can be used to keep the signal on orturn the signal off in a final image. In one embodiment, two or moresignals, resulting from the two or more excitation wavelengths can becompared and processed to calculate the desired slope. The resultingslope can be used to keep the signal on or turn the signal off in afinal image.

In one embodiment, any of the methods or systems can be used for aplurality of stains on or within a sample or fraction thereof. The stepscan be performed simultaneously for at least two of the stains or can beperformed for a first stain and then for a second stain. In oneembodiment, the first- or higher-order derivative can be calculated foreach detection moiety spectral edge. In one embodiment, the spectraledge of the respective detection moieties can be used to differentiatebetween the emissions of the different detection moieties.

In one embodiment, the minimum number of raw images is n, where n is thenumber of detection moieties. For example, a first raw image can beobtained at a higher end of a trailing edge of a first emission spectrumand at a lower end of a leading edge of a second emission spectrum. Asecond raw image can be obtained at a lower end of the trailing edge ofthe first emission spectrum and at a higher end of the leading edge ofthe second emission spectrum. The first and second raw images can beprocessed and/or analyzed to provide a first final image of a firstdetection moiety (as depicted by the first emission spectrum) and asecond final image of a second detection moiety (as depicted by thesecond emission spectrum). Though the emission spectra is discussed,this embodiment can be implemented on excitation spectra.

In one embodiment, the minimum number of raw images is n+1, where n isthe number of detection moieties.

In one embodiment, all of the raw and final images of the first andsecond detection moieties are displayed to an end user or operator, suchas on a screen (e.g., the screen of at least one of a phone, a tablet, acomputer, a television, a PDA, a handheld device, or the like). In oneembodiment, at least one of the raw images of the first and/or seconddetection moieties is displayed. In one embodiment, at least one of thefinal images of the first and/or second detection moieties is displayed.In one embodiment, none of the raw images are displayed but at least oneof the final images is displayed. In one embodiment, none of the rawimages are displayed but all of the final images are displayed.

The embodiments for acquiring signals (for example, same spectral edges,different spectral edges, peak and one spectral edge, peak and twospectral edges, etc.) are not intended to be limited to the emissionspectrum specifically discussed for the example acquisition. Rather, thesignal acquisition can apply to one or more emission spectra, whereinall emission spectra have the same acquisition (for example, samespectral edges, different spectral edges, peak and one spectral edge,peak and two spectral edges, etc.), at least two emission spectra havethe same acquisition, or no emission spectra have the same acquisition.

To obtain the raw images, the imaging can be done with a flow cytometeror a microscope, such as a fluorescent microscope, a scanner, or thelike. Imaging can be done in, conventional epifluorescence, light sheetmicroscopy, super resolution microscopy, and confocal microscopy. FIG.4A shows an optical path of a fluorescent microscope. The optical pathincludes an excitation source 402 which emits an excitation light 404,such as a light in the visible, infrared (“IR”), or ultraviolet (“UV”)spectra. The excitation light 404 comprises a plurality of wavelengths,including at least a first excitation wavelength 406 and a secondexcitation wavelength 408. The excitation light 404 interacts with anexcitation spectrum selector 410, such that the first excitationwavelength 406 passes through the excitation spectrum selector 410 andthe second excitation wavelength 408 is blocked from passing through theexcitation spectrum selector 410. The first excitation wavelength 406 isthen reflected off a second filter 412. The second filter 412 re-directsthe first excitation light 406 into an objective 414.

The objective 414 receives the first excitation wavelength 406 andfocuses the first excitation wavelength at a point or surface on,within, or near a sample or fraction thereof 434. The first excitationwavelength 406 stimulates a first detection moiety (not shown) on orwith the sample or fraction thereof 434, thereby causing the firstdetection moiety (not shown) to emit a first emission light 416 having afirst emission wavelength. The first emission light 416 can be capturedby the objective 414, passed back through the second filter 412, passedthrough an emission spectrum selector 430, and onto an emission detector440. The emission detector 440 can be a charge-coupled device (“CCD”),CMOS camera, a scientific CMOS camera, photodiode, photomultiplier tube,or the like for capturing image data, which can then be compiled intoimages, processed and analyzed by a computer or associated software orprograms.

The excitation source 402 emits the excitation light 404 again. Theexcitation light 404, however, now interacts with the excitationspectrum selector 410, such that the second excitation wavelength 408passes through the excitation spectrum selector 410 and the firstexcitation wavelength 406 is blocked from passing through the excitationspectrum selector 410. The second excitation wavelength 408 is thenreflected off the second filter 412. The second filter 412 re-directsthe second excitation light 408 into the objective 414. The objective414 receives the second excitation wavelength 408 and focuses the firstexcitation wavelength at a point or surface on, within, or near a sampleor fraction thereof 434. The second excitation wavelength 408 stimulatesthe first detection moiety (not shown) on or with the sample or fractionthereof 434, thereby causing the first detection moiety (not shown) toemit a second emission light 418 having a second emission wavelength.The second emission light 418 can be captured by the objective 414,passed back through the second filter 412, passed through the emissionspectrum selector 430, and onto an emission detector 440.

The process discussed can be performed any number of times for anynumber of detection moieties.

The second filter 412 can each be a dichroic, polychroic, bandpass,bandstop, or any appropriate filter.

The sample or fraction thereof 434 can be located on a base 432 orbetween a cover 436 and the base 432. The cover 436 and the base 432 canbe optically clear to permit imaging. The sample 434, the cover 436, andthe base 432 can be located on a platform 428 to move the sample 434 inan x-, y-, or z-direction as required. The platform 428 can include anaperture 438 which allows the first excitation wavelength 406, havingbeen focused by the objective 414, into, on, or near the sample orfraction thereof 434. The platform 428 can be driven by a driver 420,which includes at least one of a z-direction drive 424, an x-directiondrive 422, and a y-direction drive 426 to position the sample 434. Thedriver 420 can be a motor, such as a servomotor or a stepper motor, apiezo-electric actuator, a solenoid, or the like.

The optical path can also include a cut-off aperture (not shown), suchas in a confocal microscope, to increase the signal/noise ratio of theboundary light signal.

The base 432 can be composed of glass; an inert metal; a metal; ametalloid; organic or inorganic materials, and plastic materials, suchas a polymer; and combinations thereof. The cover 436 can be composed ofan optically transparent material.

FIG. 4B shows an optical path of a fluorescent microscope similar tothat of FIG. 4A, except that the excitation source 402 emits the firstand second excitation wavelengths as separate lights 406, 408.

FIG. 4C shows an optical path of a fluorescent microscope similar tothat of FIG. 4B, except that the excitation spectrum selector 410 is notincorporated into the optical path.

In one embodiment, the excitation spectrum selector 410 or the emissionspectrum selector 430 can be a filter to block or pass givenwavelengths. In one embodiment, the excitation spectrum selector 410 orthe emission spectrum selector 430 can be a notch filter, a bandstopfilter, or a bandpass filter. In one embodiment, the excitation spectrumselector 410 or the emission spectrum selector 430 can be an acoustooptic tunable filter or a liquid crystal tunable filter. In oneembodiment, the excitation spectrum selector 410 or the emissionspectrum selector 430 can be a diffraction grating. In one embodiment,the excitation spectrum selector 410 or the emission spectrum selector430 can include a filter capable of being re-angled to block or passgiven wavelengths based on the angle at which the filter is tilted,turned, or adjusted relative to an incoming light, thereby changing theangle of incidence of light upon the filter. As an example, the firstexcitation wavelength 406 passes through the excitation spectrumselector 410 and the second excitation wavelength 408 is blocked frompassing through the excitation spectrum selector 410 due to the angle ofthe excitation spectrum selector. Then, the excitation spectrum selector410 can be re-angled (θ) to block the first excitation wavelength 406and pass the second excitation wavelength 408. Though the examplediscusses the excitation spectrum selector 410, the first excitationwavelength 406, and the second excitation wavelength 408, the opticalpathway is not intended to be so limiting.

Re-angling can be applied to the emission spectrum selector 430 to blockand pass certain emission wavelengths. Additionally, rotating or anglingcan be performed before or after capturing any raw image. In oneembodiment, the emission spectrum selector 430 can include a firstemission filter 442 capable of being rotated or angled from one angle ofincidence (denoted by the longer dashed line filter 442) between thefirst filter 442 and the emission light to another angle of incidence(denoted by the shorter dashed line filter 442) between the first filter442 and the emission light, including every angle in between. Forexample, a first raw image can be obtained with the first filter 442 ata first angle of incidence. Then the first filter 442 can be re-angledfrom the first angle of incidence to a second angle of incidence. Asecond raw image can then be obtained. Additionally, in capturing atleast one more raw image, the first filter 442 can be re-angled from thesecond angle of incidence to a third angle of incidence. A third rawimage can then be obtained. Additionally, in capturing at least one moreraw image, the first filter 442 can be re-angled from the third angle ofincidence to a fourth angle of incidence. A fourth raw image can then beobtained. In one embodiment, at least two of the first, second, third,and fourth angles are the same. In one embodiment, none of the first,second, third, and fourth angles are the same.

In one embodiment, the emission spectrum selector 430 can include two ormore emission filters 442, 444 such that each one is capable of beingrotated or angled. The first filter 442 can be rotated or angled fromone angle of incidence (denoted by the longer dashed line filter 442)between the first filter 442 and the emission light to another angle ofincidence (denoted by the shorter dashed line filter 442, 442) betweenthe first filter 442 and the emission light, including every angle inbetween. The second filter 444 can be rotated or angled from a one angleof incidence (denoted by the longer dashed line filter 444) between thesecond filter 444 and the emission light to another angle of incidence(denoted by the shorter dashed line filter 444) between the secondfilter 444 and the emission light, including every angle in between. Thefirst and second filters 442, 444 can be rotated or angled independentlyof each other. In other words, the first filter 442 can have any numberof positions (i.e., first position, second position, third position,fourth position, and so on until the n^(th) position) with each positioncorresponding to a different angle. The second filter 444 can have anynumber of positions (i.e., first position, second position, thirdposition, fourth position, and so on until the n^(th) position) witheach position corresponding to a different angle. Each filter 442, 444can have a position (or angle) independent of the other filter, suchthat one or both filters 442, 444 can be angled or rotated, and suchthat the filters 442, 444 can have the same angle of incident ordifference angles of incidence. The filters 442, 444 can be positionedor angled to obtain desired wavelengths.

For example, a first raw image can be obtained with the first filter 442at a first angle of incidence and the second filter 444 at a third angleof incidence. Then the first filter 442 can be re-angled from the firstangle of incidence to a second angle of incidence, while the secondfilter 444 stays at the third angle of incidence. A second raw image canthen be obtained. Additionally, in capturing at least one more rawimage, the second filter 442 can be re-angled from the third angle ofincidence to a fourth angle of incidence. A third raw image can then beobtained. In one embodiment, at least two of the first, second, third,and fourth angles are the same. In one embodiment, none of the first,second, third, and fourth angles are the same.

In any of the embodiments including rotating or angling at least onefilter, any filter can be rotated or angled at any desired time or stepto obtain a desired emission wavelength. For example, after obtaining afirst raw image with the first and second filters 442, 444 at first andthird angles of incidence, respectively, the first and second filters442, 444 can be rotated or angled to second and fourth angles ofincidence, respectively. A second raw image can then be obtained. Then,one or both of the filters 442, 444 can be rotated or angled. A thirdraw image can be obtained. In other words, each filter can be rotated orangled independently of the other filter or filters at any point and byany amount to obtain any raw image and/or any desired emissionwavelength.

In one embodiment, a plurality of filters can be used, wherein thefilters have narrow bandpass (for example, 1 nm, 2 nm, 3 nm, 5 nm, 10nm, 20 nm, 25 nm, or 50 nm; 1-50 nm; or the like). Therefore, inaddition to or instead of rotating, the filters can be changed in andout to provide desired emission or excitation wavelengths.

Furthermore, though one and two filters are discussed, any number offilters can be used, including, without limitation, 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, or 100.

Though the examples and embodiments discussed herein are applied to theemission spectrum selector 430, one or more filters capable of beingrotated or angled, and the methods of using the same, can also beapplied to the excitation spectrum selector 410. Accordingly, in oneembodiment, at least one of the excitation and emission spectrumselectors 410, 430 can include at least one filter capable of beingrotated or angled. In one embodiment, one of the excitation and emissionspectrum selectors 410, 430 can include at least one filter capable ofbeing rotated or angled. In one embodiment, both of the excitation andemission spectrum selectors 410, 430 can include at least one filtercapable of being rotated or angled.

The individual filters of the excitation spectrum selector 410 or theemission spectrum selector 430 or the angle of incidence between thefilters and the excitation or emission light can be selected to thedesired raw images at the lower and higher edges of the desired spectraledges. For example, in one embodiment, the detection moieties can havedifferences in spectra at their peaks of less than or equal to 50 nm. Inone embodiment the detection moieties can have differences in spectra attheir peaks of less than or equal to 10 nm. In one embodiment, thedetection moieties can have differences in spectra at their peaks of1-50 nm. In one embodiment, the detection moieties can have differencesin spectra at their peaks of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15,20, 25, 30, 40, 50, 60, 70, 75, 80, 90, or 100 nm. In one embodiment,the difference between successive spectra (such as at the peak) can bethe same (e.g., first and second detection moieties are separated by 10nm and second and third detection moieties are separated by 10 nm). Inone embodiment, the differences between successive spectra (such as atthe peak) can be different (e.g., first and second detection moietiesare separated by 10 nm and second and third detection moieties areseparated by 25 nm).

In one embodiment, the angle of incidence of light upon any filter canbe 0.0°, 1.0°, 2.0°, 3.0°, 4.0°, 5.0°, 6.0°, 7.0°, 8.0°, 9.0°, 10.0°,11.0°, 12.0°, 15.0°, 20.0°, 25.0°, 30.0°, 40.0°, 45.0°, 50.0°, 60.0°,70.0°, 75.0°, 80.0°, 85.0°, or 89.9°. In one embodiment, the angle ofincidence of light upon any filter can be up to, but not inclusive of,90°. In one embodiment, the angle of incidence of light upon any filtercan be less than 90°. In one embodiment, the angle of incidence of lightupon any filter can be from 0.0° to 89.9°. As noted above, when thereare two or more filters, each filter rotates freely and independently ofthe other filters, such that two or more filters can have the same angleof incidence or no two filters have the same angle of incidence. Theangles of incidence are selected based on the desired wavelength to beobtained.

Any of the images or files, whether raw or processed, can be stored inany appropriate storage medium at any point during the performance ofany embodiment of the present invention. The storage medium includes,but is not limited to, one or more of a hard disk, a random-accessmemory (RAM), a read only memory (ROM), a storage of distributedcomputing systems, an optical disk (such as a compact disc, digitalversatile disc, or Blu-ray Disc), a flash memory device, a memory card,or the like.

Embodiments of the invention include a non-transitory computer readablemedium which can store instructions for performing the above-describedmethods and any steps thereof, including any combinations of the same.For example, the non-transitory computer readable medium can storeinstructions for execution by one or more processors or similar devices.

Embodiments of the invention include two or more non-transitory computerreadable media which can store instructions for performing theabove-described methods and any steps thereof, including anycombinations of the same. For example, the instructions for executioncan be split amongst two or more processors or similar devices.

Further embodiments of the present invention can also include a computeror apparatus (e.g. a phone, a tablet, a PDA, or the like) which readsout and executes computer executable instructions, such as anon-transitory computer-readable medium, recorded or stored on a storagemedium (which may be the same as or different than the storage mediumfor storing images or files, as discussed above), to perform thefunctions of any embodiment. The computer may include one or more of acentral processing unit (CPU), micro processing unit (MPU), or othercircuitry, and may include a network of separate computers or separatecomputer processors. The computer executable instructions may beprovided to the computer, for example, from a network or the storagemedium.

The computer or apparatus can also be configured to display, such as ona monitor or screen, any of the images or files, whether raw orprocessed.

EXAMPLE(S)

A sample labeled with Sytox Orange and CF 568 is provided and imaged.FIG. 5A shows a first raw image at emission wavelength 550 nm (+/−5 nm).FIG. 5B shows a second raw image at emission wavelength 570 nm (+/−5nm). FIG. 5C shows a third raw image at emission wavelength 590 nm (+/−5nm). One or more signals within the first, second, and third raw imagesare provided by one or more of autofluorescence, Sytox Orange, and CF568. FIG. 5E shows a final image of Sytox Orange after the first,second, and third raw images undergo analysis and processing based onemission curvatures, as discussed above, to at least partially, if notcompletely, remove signals caused by autofluorescence and CF 568.

The sample labeled with Sytox Orange and CF 568 is provided and imaged.FIG. 5B shows the second raw image at emission wavelength 570 nm (+/−5nm). FIG. 5D shows a fourth raw image at emission wavelength 600 nm(+/−5 nm). One or more signals within the second and fourth raw imagesare provided by one or more of autofluorescence, Sytox Orange, and CF568. FIG. 5F shows a final image of CF 568 after at least two of thefirst, second, third, and fourth raw images undergo analysis andprocessing based on emission slopes, as discussed above, to at leastpartially, if not completely, remove signals caused by autofluorescenceand Sytox Orange.

FIG. 5G shows a final image of the autofluorescence after at least twoof the first, second, third, and fourth raw images undergo analysis andprocessing based on emission curvatures, as discussed above, to at leastpartially, if not completely, remove signals caused by the Sytox Orangeand CF 568. In other words, FIG. 5G depicts the autofluorescence of aparticular structure of the sample.

When a feature or element is herein referred to as being “on” anotherfeature or element, it can be directly on the other feature or elementor intervening features and/or elements may also be present. Incontrast, when a feature or element is referred to as being “directlyon” another feature or element, there are no intervening features orelements present. It will also be understood that, when a feature orelement is referred to as being “connected”, “attached” or “coupled” toanother feature or element, it can be directly connected, attached orcoupled to the other feature or element or intervening features orelements may be present. In contrast, when a feature or element isreferred to as being “directly connected”, “directly attached” or“directly coupled” to another feature or element, there are nointervening features or elements present. Although described or shownwith respect to one embodiment, the features and elements so describedor shown can apply to other embodiments. It will also be appreciated bythose of skill in the art that references to a structure or feature thatis disposed “adjacent” another feature may have portions that overlap orunderlie the adjacent feature.

Terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention.For example, as used herein, the singular forms “a”, “an” and “the” areintended to include the plural forms as well, unless the context clearlyindicates otherwise. It will be further understood that the terms“comprises” and/or “comprising,” when used in this specification,specify the presence of stated features, steps, operations, elements,and/or components, but do not preclude the presence or addition of oneor more other features, steps, operations, elements, components, and/orgroups thereof. As used herein, the term “and/or” includes any and allcombinations of one or more of the associated listed items and may beabbreviated as “/”.

Spatially, graphically, or numerically relative terms, such as “under”,“below”, “lower”, “over”, “upper”, “higher”, and the like, may be usedherein for ease of description to describe one element or feature'srelationship to another element(s) or feature(s) as illustrated in thefigures. It will be understood that the spatially relative terms areintended to encompass different orientations when in use or operation inaddition to the orientation depicted in the figures. For example, if adevice, system, or method, as depicted in the figures is inverted,elements described as “under” or “beneath” other elements or featureswould then be oriented “over” the other elements or features. Thus, theexemplary term “under” can encompass both an orientation of over andunder. The device may be otherwise oriented (rotated 90 degrees or atother orientations) and the spatially relative descriptors used hereininterpreted accordingly. Similarly, the terms “upwardly”, “downwardly”,“vertical”, “horizontal” and the like are used herein for the purpose ofexplanation only unless specifically indicated otherwise. Additionally,“lower”, “higher”, and the like are used to depict elements, features,information, or the like which, relative to each other or at least otherelements, features, information, or the like are further down or furtherup a chart, graph, or plot, or are lesser or greater in value orintensity.

Although the terms “first” and “second” may be used herein to describevarious features/elements (including steps), these features/elementsshould not be limited by these terms, unless the context indicatesotherwise. These terms may be used to distinguish one feature/elementfrom another feature/element. Thus, a first feature/element discussedbelow could be termed a second feature/element, and similarly, a secondfeature/element discussed below could be termed a first feature/elementwithout departing from the teachings of the present invention.Additionally, though “first” and “second” are used, the terms are notintended to limit various features/elements to only one or two. Rather,three (i.e., third), four (i.e., fourth), or more may be included orused where appropriate or desirous to do so.

Throughout this specification and the claims which follow, unless thecontext requires otherwise, the word “comprise”, and variations such as“comprises” and “comprising” means various components can be co-jointlyemployed in the methods and articles (e.g., compositions and apparatusesincluding device and methods). For example, the term “comprising” willbe understood to imply the inclusion of any stated elements or steps butnot the exclusion of any other elements or steps.

As used herein in the specification and claims, including as used in theexamples and unless otherwise expressly specified, all numbers may beread as if prefaced by the word “about” or “approximately,” even if theterm does not expressly appear. The phrase “about” or “approximately”may be used when describing magnitude and/or position to indicate thatthe value and/or position described is within a reasonable expectedrange of values and/or positions. For example, a numeric value may havea value that is +/−0.1% of the stated value (or range of values), +/−1%of the stated value (or range of values), +/−2% of the stated value (orrange of values), +/−5% of the stated value (or range of values), +/−10%of the stated value (or range of values), etc. Any numerical valuesgiven herein should also be understood to include about or approximatelythat value, unless the context indicates otherwise. For example, if thevalue “10” is disclosed, then “about 10” is also disclosed. Anynumerical range recited herein is intended to include all sub-rangessubsumed therein. It is also understood that when a value is disclosedthat “less than or equal to” the value, “greater than or equal to thevalue” and possible ranges between values are also disclosed, asappropriately understood by the skilled artisan. For example, if thevalue “X” is disclosed the “less than or equal to X” as well as “greaterthan or equal to X” (e.g., where X is a numerical value) is alsodisclosed. It is also understood that the throughout the application,data is provided in a number of different formats, and that this data,represents endpoints and starting points, and ranges for any combinationof the data points. For example, if a particular data point “10” and aparticular data point “15” are disclosed, it is understood that greaterthan, greater than or equal to, less than, less than or equal to, andequal to 10 and I₅ are considered disclosed as well as between 10 and15. It is also understood that each unit between two particular unitsare also disclosed. For example, if 10 and I₅ are disclosed, then 11,12, 13, and 14 are also disclosed.

Although various illustrative embodiments are described above, any of anumber of changes may be made to various embodiments without departingfrom the scope of the invention as described by the claims. For example,the order in which various described method steps are performed mayoften be changed in alternative embodiments, and in other alternativeembodiments one or more method steps may be skipped altogether. Optionalfeatures of various device and system embodiments may be included insome embodiments and not in others. Therefore, the foregoing descriptionis provided primarily for exemplary purposes and should not beinterpreted to limit the scope of the invention as it is set forth inthe claims.

The examples and illustrations included herein show, by way ofillustration and not of limitation, specific embodiments in which thesubject matter may be practiced. As mentioned, other embodiments may beutilized and derived there from, such that structural and logicalsubstitutions and changes may be made without departing from the scopeof this disclosure. Such embodiments of the inventive subject matter maybe referred to herein individually or collectively by the term“invention” merely for convenience and without intending to voluntarilylimit the scope of this application to any single invention or inventiveconcept, if more than one is, in fact, disclosed. Thus, althoughspecific embodiments have been illustrated and described herein, anyarrangement calculated to achieve the same purpose may be substitutedfor the specific embodiments shown. This disclosure is intended to coverany and all adaptations or variations of various embodiments.Combinations of the above embodiments, and other embodiments notspecifically described herein, will be apparent to those of skill in theart upon reviewing the above description.

The foregoing description, for purposes of explanation, used specificnomenclature to provide a thorough understanding of the disclosure.However, it will be apparent to one skilled in the art that the specificdetails are not required in order to practice the systems and methodsdescribed herein. The foregoing descriptions of specific embodiments arepresented by way of examples for purposes of illustration anddescription. They are not intended to be exhaustive of or to limit thisdisclosure to the precise forms described. Many modifications andvariations are possible in view of the above teachings. The embodimentsare shown and described in order to best explain the principles of thisdisclosure and practical applications, to thereby enable others skilledin the art to best utilize this disclosure and various embodiments withvarious modifications as are suited to the particular use contemplated.It is intended that the scope of this disclosure be defined by thefollowing claims and their equivalents:

What is claimed is:
 1. A method of analyzing a sample, the samplecomprising a first component, the first component having a firstautofluorescent emission spectrum, the first autofluorescent emissionspectrum having a peak emission intensity at a peak intensitywavelength, a leading spectral edge with emission intensities less thanthe peak intensity at wavelengths less than the peak intensitywavelength, and a trailing spectral edge with emission intensities lessthan the peak intensity at wavelengths greater than the peak intensitywavelength, the method comprising: acquiring, by stimulating the samplewith excitation light, a first raw image of the sample at a firstemission wavelength of the first autofluorescent emission spectrum ofthe first component, wherein the first emission wavelength is in theleading spectral edge or in the trailing spectral edge of the firstautofluorescent emission spectrum, and wherein the first raw imagecomprises a first total signal comprising a first autofluorescent signalat the first emission wavelength; acquiring, by stimulating the samplewith excitation light, a second raw image of the sample at a secondemission wavelength of the first autofluorescent emission spectrum ofthe first component, wherein the second raw image comprises a secondtotal signal comprising a second autofluorescent signal at the secondemission wavelength; and outputting a final image of the first componentbased on the first and second raw images, and wherein the firstcomponent comprises a non-detection moiety.
 2. The method of claim 1,wherein the second emission wavelength is at the peak intensity of thefirst autofluorescent emission spectrum, and wherein the emissionintensity at the first emission wavelength is less than the emissionintensity at the second emission wavelength.
 3. The method of claim 1,wherein the second emission wavelength is in the same spectral edge ofthe first autofluorescent emission spectrum as the first emissionwavelength, and wherein the emission intensity at the first emissionwavelength is less than the emission intensity at the second emissionwavelength.
 4. The method of claim 1, wherein the second emissionwavelength is in a different spectral edge of the first autofluorescentemission spectrum than the first emission wavelength, and wherein theemission intensity at the first emission wavelength is less than theemission intensity at the second emission wavelength.
 5. The method ofclaim 1, wherein the second emission wavelength is in a differentspectral edge of the first autofluorescent emission spectrum than thefirst emission wavelength, and wherein the emission intensity at thefirst emission wavelength is the same as the emission intensity at thesecond emission wavelength.
 6. The method of claim 1, the sample furthercomprising one or more detection moieties, wherein at least one of thefirst and second total signals further comprises one or more signalscaused by the one or more detection moieties.
 7. The method of claim 1,wherein the sample further comprises a second component having a secondautofluorescent emission spectrum, the second autofluorescent emissionspectrum having a peak emission intensity at a peak intensitywavelength, a leading spectral edge with emission intensities less thanthe peak intensity at wavelengths less than the peak intensitywavelength, and a trailing spectral edge with emission intensities lessthan the peak intensity at wavelengths greater than the peak intensitywavelength, wherein at least one of the first and second total signalsfurther comprises an autofluorescent signal caused by the secondcomponent, and wherein the second component comprises a non-detectionmoiety.
 8. The method of claim 7, further comprising outputting a finalimage of the second component based on the first and second raw images.9. The method of claim 7, wherein the first emission wavelength at whichthe first raw image is acquired is in the leading spectral edge or thetrailing spectral edge of the second autofluorescent emission spectrum,wherein the second emission wavelength at which the second raw image isacquired is in the same leading spectral edge or the same trailing edgeof the second autofluorescent emission spectrum as the first emissionwavelength, and wherein the second autofluorescent emission spectrum hasa lower emission intensity for the first emission wavelength than forthe second emission wavelength.
 10. The method of claim 9, furthercomprising acquiring, by stimulating the sample with excitation light, athird raw image of the sample at a third emission wavelength of thesecond autofluorescent emission spectrum, wherein the third emissionwavelength is at the peak intensity wavelength of the secondautofluorescent emission spectrum, and wherein the third raw imagecomprises a third total signal comprising a second component signal atthe peak intensity wavelength of the second component.
 11. The method ofclaim 10, further comprising outputting a final image of the secondcomponent based on at least two of the first, second, and third rawimages.
 12. The method of claim 7, wherein the first emission wavelengthat which the first raw image is acquired is in the leading spectral edgeor the trailing spectral edge of the second autofluorescent emissionspectrum, wherein the second emission wavelength at which the second rawimage is acquired is at the peak intensity of the second autofluorescentemission spectrum, and wherein the second autofluorescent emissionspectrum has a lower emission intensity for the first emissionwavelength than for the second emission wavelength.
 13. The method ofclaim 12, further comprising acquiring, by stimulating the sample withexcitation light, a third raw image of the sample at a third emissionwavelength of the second autofluorescent emission spectrum, wherein thethird emission wavelength is in a different spectral edge of the secondautofluorescent emission spectrum than the first emission wavelength,and wherein the third raw image comprises a third total signalcomprising a second component signal at the third emission wavelength ofthe second component.
 14. The method of claim 13, further comprisingoutputting a final image of the second component based on at least twoof the first, second, and third raw images.
 15. The method of claim 7,wherein the first emission wavelength at which the first raw image isacquired is in the leading spectral edge or the trailing spectral edgeof the second autofluorescent emission spectrum, wherein the secondemission wavelength at which the second raw image is acquired is in adifferent spectral edge of the second autofluorescent emission spectrumthan the first emission wavelength.
 16. The method of claim 15, furthercomprising acquiring, by stimulating the sample with excitation light, athird raw image of the sample at a third emission wavelength of thesecond autofluorescent emission spectrum, and wherein the third rawimage comprises a third total signal comprising a second componentsignal at the third emission wavelength of the second component.
 17. Themethod of claim 16, further comprising outputting a final image of thesecond component based on at least two of the first, second, and thirdraw images.
 18. The method of claim 7, wherein the leading edge of thefirst autofluorescent emission spectrum and the leading edge of thesecond autofluorescent emission spectrum have an offset of 1-200 nm,wherein the offset is the difference between wavelengths of the leadingedge of the first autofluorescent emission spectrum and the leading edgeof the second autofluorescent emission spectrum having the same emissionintensity.
 19. The method of claim 7, further comprising outputting afinal image of the second component based on the first and second rawimages.
 20. The method of claim 7, wherein the first component is anucleus, cytoplasm, cytosol, a cell membrane, a cell wall, a fiber,cartilage, a cell, an interstitial fluid, a protein, a glycoproteins, apeptide, a carbohydrate, a nucleic acid, a cytochrome, a flavin,collagen, a lipid, a biomolecule, an intra-cellular deposit, anextra-cellular deposit, or material foreign to a biological sample. 21.The method of claim 1, further comprising displaying, on a screen, atleast one of the first raw image, the second raw image, and the finalimage of the first component to an end user or operator.
 22. The methodof claim 1, further comprising the steps of selecting, with one or moreautofluorescent emission spectrum selectors, the first emissionwavelength from a first emission light comprising the first emissionwavelength, and capturing the first emission wavelength with a detector,wherein selecting and capturing the first emission wavelength aresub-steps of the step for acquiring the first emission wavelength. 23.The method of claim 1, wherein the first total signal is acquired at afirst pixel of the first image, wherein the second total signal isacquired at a second pixel of the second image, and wherein the firstand second pixels correspond to an identical location on or within thesample.
 24. The method of claim 1, further comprising acquiring, bystimulating the sample with excitation light, a third raw image of thesample at a third emission wavelength of the first autofluorescentemission spectrum.
 25. The method of claim 24, wherein one of the first,second, and third raw images is at the peak intensity of the firstautofluorescent emission spectrum.
 26. The method of claim 25, whereinthe other two raw images are in the same leading or trailing spectral aseach other.
 27. The method of claim 25, wherein the other two raw imagesare in different spectral edges of the first autofluorescent emissionspectrum than each other.
 28. The method of claim 24, wherein at leasttwo of the first, second, and third raw images are in the same spectraledge of the first autofluorescent emission spectrum.
 29. The method ofclaim 24, wherein the first, second, and third raw images are in thesame spectral edge of the first autofluorescent emission spectrum.
 30. Anon-transitory computer readable medium comprising instructions to causeone or more processors or devices to perform a method of analyzing asample, the sample comprising a first component, the first componenthaving a first autofluorescent emission spectrum, the firstautofluorescent emission spectrum having a peak emission intensity at apeak intensity wavelength, a leading spectral edge with emissionintensities less than the peak intensity at wavelengths less than thepeak intensity wavelength, and a trailing spectral edge with emissionintensities less than the peak intensity at wavelengths greater than thepeak intensity wavelength, the method comprising: acquiring, bystimulating the sample with excitation light, a first raw image of thesample at a first emission wavelength of the first autofluorescentemission spectrum of the first component, wherein the first emissionwavelength is in the leading spectral edge or in the trailing spectraledge of the first autofluorescent emission spectrum, and wherein thefirst raw image comprises a first total signal comprising a firstautofluorescent signal at the first emission wavelength; acquiring, bystimulating the sample with excitation light, a second raw image of thesample at a second emission wavelength of the first autofluorescentemission spectrum of the first component, wherein the second emissionwavelength, and wherein the second raw image comprises a second totalsignal comprising a second autofluorescent signal at the second emissionwavelength; and outputting a final image of the first component based onthe first and second raw images, and wherein the first componentcomprises a non-detection moiety.
 31. The method of claim 10, the samplefurther comprising one or more detection moieties, wherein at least oneof the first, second, and third total signals further comprises one ormore signals caused by the one or more detection moieties.
 32. Themethod of claim 13, the sample further comprising one or more detectionmoieties, wherein at least one of the first, second, and third totalsignals further comprises one or more signals caused by the one or moredetection moieties.